Bayesian Statistics
These following conditional statistics are based upon all of the DNA detection system results that were obtained in the PCR lab for 20 hypothetical patients who were diagnosed as either having cancer or not having cancer.

Bayes Theorem equation: P(A|B) = P(B|A) * P(A) / P(B)

Calculation 1: The probability that the sample actually has the cancer DNA sequence, given a positive diagnostic signal.

Calculation 3: The probability that the patient will develop cancer, given a cancer DNA sequence.

A = frequency of "yes" cancer diagnosis = 9 / 20 = 0.45

B = frequency of "pos" test conclusion = 26 / 60 = 0.43

P (B|A) = frequency of pos given yes = 24 / 26 = 0.92

P(A|B) = 0.96 = 96%

Calculation 4: The probability that the patient will not develop cancer, given a non-cancer DNA sequence.

A = frequency of "no" cancer diagnosis = 11 / 20 = 0.55

B = frequency of "neg" test conclusion = 34 / 60 = 0.57

P (B|A) = frequency of neg given no = 31 / 34 = 0.91

P(A|B) = 0.88 = 88%

New System: Design Strategy

We concluded that a good system Must Have:

- easily determined results: The easier the results are to read accurately, the less likely a misdiagnosis in either direction. It is undesirable both to give a false negative, where a patient is not treated when care is needed, or to give a false positive, wasting time and resources on those who do not need them. This aspect is central to any diagnostic tool.

- Simple OpenPCR Software: Simplicity increases ease and efficiency in lab experiments and hopefully leads to faster diagnoses. It also makes troubleshooting easier should problems arise. The more straightforward the system, the more quickly users can learn to use the machine.

We concluded that we would Want a good system to have:

- Low cost: Currently an OpenPCR machine costs $599 and a Fluorimeter costs $300. An inexpensive material would help reduce cost and increase accessibility, since there is always a limited budget for new equipment. This would not only allow users to increase the amount of tests that can be run at the same time, but also boost sales, which is important for marketing any device.

- integrated camera: phone cameras are easily moveable and vary in size and quality, leading to differing results. Smartphone camera settings can be time consuming or nonexistent. Having a built-in camera increases cost, but it is worth it to increase speed and accuracy. Furthermore, the program is simpler because it does not have to adjust to different cameras and phone sizes and shapes vary enough to make building a cradle to fit them difficult.

We concluded that a good system Must Not Have:

- Troublesome USB Connectivity. USB connectivity should function well in order for OpenPCR machine to work.

- Casing = fire hazard. High temperature with PCR can be dangerous.

We concluded that a good system Should Avoid:

- Avoid slow amplification.

- Hard to adjust phone/ fluorimeter. The phone can be easily moved by accident, which requires readjustment between the phone and the fluorimeter.

New System: Machine/ Device Engineering

SYSTEM DESIGN

Current design of fluorimeter

Rather than drastically change a fairly-efficient PCR machine, we decided that the fluorimeter setup was more in need of modification. The only change to the PCR machine would be improved USB ports, but the fluorimeter would have a built-in camera to remove the complications of positioning a camera phone. The phone would still be used to run the machine, but it wouldn't directly take the pictures. This new camera would take the place of the current cradle and be at a fixed position in respects to the fluorimeter for most efficient photographing. Also, the slots on the board of the fluorimeter would be labeled to avoid confusion in the process of analysis.

PCR Machine: We chose keep the devices the same as the original system

Reliable Hardware - the machine is sturdy and does its job efficiently considering its simple construction

Preexisting Software - the current Open PCR software is well developed and user-friendly

INSTRUCTIONS

Step 1: Connect the camera unit to the fluorimeter.

Step 2: Adjust the camera settings according to the current experiment.

Step 3: Link the camera to the phone being used to control the experiment.

Step 4: Take photo.

Step 5: Upload photo for necessary manipulation.

New System: Protocols

DESIGN

We chose to add an extra device to the fluorimeter. However, protocols should remain the same.

MATERIALS

Supplied in the Kit

Amount

Smart phone

1

Reaction mix

given more for more reactions

Battery

Software

Supplied in the User

Amount

Filter water

SYBR Green

Primers

DNA sample (negative and positive)

PROTOCOLS

PCR Protocol

Step 1: Reaction mix

Step 2: Add 2.5 μL of negative and positive DNA sample

Step 3: Fluorometer gave the sample result

DNA Measurement and Analysis Protocol

Step 1: Set up the equipment

Step 2: Put the smart phone and fluorometer in the dark box

Step 3: Major the distance between the fluorometer and phone.

Step 4: Run the samples

Step 5: Take a picture of the experiment

Step 6: Repeat this trial with different samples

Step 7: Use Image J and make a circle around the drop.

New System: Research and Development

BACKGROUND

CHEK2 is a gene located at chromosome 22. It provides instructions for making protein call checkpoint kinase 2. The checkpoint kinase acts as a tumor suppressor. Mutations of CHEK2 gene can lead to breast cancer, Li-Fraumeni syndrome, and other type cancers and diseases.

DESIGN

Primers for PCR

GGAAGTGGGTCCTAAAAACTCTTACA[C/T]TGCATACATAGAAGATCACAGTGGC

Our primers address the following design needs

Design specification 1 - explanation of how an aspect of the primers addresses any of the specifications in the "New System: Design Strategy" section

Design specification 2 - explanation of how an aspect of the primers addresses any of the specifications in the "New System: Design Strategy" section

Etc.

New System: Software

[THIS SECTION IS OPTIONAL. If your team has creative ideas for new software, and new software is a key component included in your new protocols, R&D, or machine design, you may describe it here. You will not receive bonus points, but a solid effort may raise your overall page layout points. If you decide not to propose new software, please delete this entire section, including the ==New System: Software== header.]